基于宏基因组学研究戊糖片球菌368对杜撒猪粪便微生物群落结构及基因功能的影响

Effects of Pediococcus pentosaceus 368 on the microbial community structure and gene function of Dusa pig feces based on metagenomic technology

  • 摘要: 【目的】 基于宏基因组学探究戊糖片球菌368对杜撒猪粪便微生物群落结构及基因功能的影响,为揭示戊糖片球菌368潜在的益生功能及作用机制提供理论依据。【方法】 选用体重接近的杜撒猪,按性别平衡原则随机分为对照组(FC)和试验组(FA),每组2个重复,每个重复5头杜撒猪。饲喂相同基础饲粮,FA组饮水中添加戊糖片球菌368。试验周期28 d,试验开始及结束当天,禁食12 h后称重,记录采食情况。试验结束后计算平均日增重、平均日采食量和料重比。试验结束后,各重复随机选取3头杜撒猪,采集新鲜粪便。通过宏基因组测序分析戊糖片球菌368对杜撒猪粪便微生物群落结构及基因功能。【结果】 FA组杜撒猪平均日采食量和平均日增重高于FC组,料重比低于FC组,但差异不显著(P>0.05)。Alpha多样性指数分析结果显示,FA组Shannon指数显著高于FC组(P˂0.05,下同),Simpson指数极显著高于FC组(P˂0.01)。Beta多样性分析结果显示,FA和FC组样本在坐标空间中既有重叠部分又有分离部分,FA组微生物群落在保持相似性的同时发生了一定变化。在属分类水平上,FA和FC组相对丰度最高的均为普雷沃氏菌属(Prevotella_copri)。LEfSe分析结果显示,当LDA>3.0时,FA组获得14个生物标志物,FC组获得6个生物标志物。KEGG数据库注释分析结果显示,LDA>3.0时,信号转导和氨基酸代谢2条信号通路仅在FA组注释到基因。CAZy数据库注释分析结果显示,在1级水平上,FA组辅助氧化还原酶信号通路注释到的基因数量显著高于FC组;在2级水平上,FA和FC组间注释到基因数量差异显著的信号通路有30条,与FC组相比,FA组中26条信号通路注释到的基因数量显著上调;当LDA>2.0时,筛选出4种相关基因,其中CBM61GT58GH13_9属于FA组,GH0属于FC组。CARD抗性基因分析结果显示,当LDA>2.0时,筛选出3类差异抗性基因,FC组抗性基因主要富集于碳青霉烯类水解β-内酰胺酶,FA组抗性基因主要富集于vga type ABC F potein和糖肽抗性基因簇。【结论】 饮水中添加戊糖片球菌368能提高杜撒猪生长性能,并改变其粪便微生物群落组成,提升厚壁菌及梭菌等优势菌群的相对丰度,还能提高与复杂碳水化合物代谢相关的GH13、GH96和GH84等家族基因相对丰度。戊糖片球菌368可能具有促进复杂碳水化合物代谢相关菌群与酶类表达的潜在益生作用。

     

    Abstract: 【Objective】 Based on metagenomics,the effects of Pediococcus pentosaceus 368 on the fecal microbial community structure and gene function of Dusa pigs were explored,in order to reveal the potential prebiotic function of Pediococcus pentosaceus 368 and theoretical basis for its mechanism of action. 【Method】 Dusa pigs with similar body weight were selected and randomly divided into a control group(FC)and an experimental group(FA)according to the principle of gender balance,with 2 replicates in each group and 5 Dusa pigs in each replicate. The same basal diet was fed,and Pediococcus pentosaceus 368 was added to the drinking water of the FA group. The experimental period was 28 d. On the days of the start and end of the experiment,the pigs were weighed after fasting for 12 h,and the feeding situation was recorded. After the end of the experiment,the average daily weight gain,average daily feed intake and feed to weight ratio were calculated. After the end of the experiment,3 Dusa pigs were randomly selected from each replicate and fresh feces were collected. The effect of Pediococcus pentosaceus 368 on the fecal microbial community structure and gene function of Dusa pigs was analyzed by metagenomic sequencing technology. 【Result】 The average daily feed intake and average daily weight gain of Dusa pigs in the FA group were higher than those in the FC group,and the feed to weight ratio was lower than that in the FC group,but the difference was not significant(P>0.05). The results of Alpha diversity index analysis showed that the Shannon index of the FA group was significantly higher than that of the FC group(P˂0.05, the same below),and the Simpson index was extremely significantly higher than that of the FC group(P˂0.01). The results of Beta diversity analysis showed that the samples of the FA and FC groups had both overlapping and separated parts in the coordinate space,and the microbial community of the FA group had some changes while maintaining similarity. At the genus level,the genus Prevotella_copri had the highest relative abundance in both the FA and FC groups. The results of LEfSe analysis showed that when LDA>3.0 ,14 biomarkers were obtained in the FA group and 6 biomarkers were obtained in the FC group. KEGG database annotation analysis found that when LDA>3.0,the 2 signal pathways of signal transduction and amino acid metabolism annotated to genes only in the FA group. CAZy database annotation analysis found that at the level 1,the number of genes annotated to the auxiliary oxidoreductase signaling pathway in the FA group was significantly higher than that in the FC group;at the level 2,there were 30 signaling pathways with significant differences in the number of genes annotated between the FA and FC groups,and the number of genes annotated to 26 signa-ling pathways in the FA group was significantly up-regulated compared with the FC group. When LDA>2.0,4 related genes were screened out,of which CBM61CT58 and GH13_9 belonged to the FA group,and GH0 belonged to the FC group. CARD resistance gene analysis results showed that when LDA>2.0,3 types of differential resistance genes were screened out,and the resistance genes in the FC group were mainly enriched in carbapenem hydrolyzing β-lactamase,and the resistance genes in the FA group were mainly enriched in vga type ABC F potein and glycopeptide resistance gene clusters. 【Conclusion】 Adding Pediococcus pentosaceus 368 to drinking water can improve the growth performance of Dusa pigs and change the composition of their fecal microbial community,increase the relative abundance of dominant bacteria such as Firmicutes and Clostridiales. It can also increase the relative abundance of family genes such as GH13, GH96 and GH84 related to complex carbohydrate metabolism,Pediococcus pentosaceus 368 may have a potential probiotic effect in promoting the expression of bacteria and enzymes related to complex carbohydrate metabolism.

     

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